There is, indeed, a stripped-down version of jQuery v1.7.0 included within the 'juicebox.js' file.
However, it is not possible for a user to manually remove or replace this version of jQuery.
I have notified the developers of your post and I'm sure they will investigate further.
Thank you for the report.

I'm glad you've got it working.
Thank you for posting back to let me know.

As far as I can recall, only three other users have reported such a problem before (in differing versions of Lightroom and the Juicebox Plugin) and two of these users reported that they were using Mac OS X 10.11 (the other user's operating system is unknown).
Please see these forum threads:
https://juicebox.net/forum/viewtopic.php?id=2115
https://juicebox.net/forum/viewtopic.php?id=2249

Please let me know what operating system you use (and also what version of the Juicebox Plugin you use) so that we can gather more data about the problem. If you are not already using the latest version of the plugin (v1.5.1), then I would recommend upgrading to see if this makes a difference.
The Juicebox Plugin for Lightroom can be found inside the Juicebox-Pro zip package and instructions for downloading the latest version of Juicebox-Pro can be found on the Upgrading Juicebox support page. (Instructions for installing the plugin can be found here.)

Unfortunately, I have never been able to replicate the problem myself on my own Windows 10 PC and it is difficult to troubleshoot a problem which I cannot reproduce.

When the problem next occurs, try reloading the live preview window by pressing Cmd+R (Mac), Ctrl+R (Windows) or by selecting 'Web -> Reload' from the drop-down menu at the top. Hopefully this will clear the problem.

Another workaround might be to prevent the live preview window from being updated each time a configuration option is changed and, instead, update the live preview window manually (whenever required) by pressing Cmd+R (Mac), Ctrl+R (Windows) or by selecting 'Web -> Reload' from the drop-down menu at the top.
Disabling the instant update functionality to the live preview window (and reloading the web page only on demand) should hopefully help (even though it might not be an ideal solution).

If you'd like to try it, download the 'galleryInfo.lrweb' file from here and use it to replace your plugin's existing 'galleryInfo.lrweb' file (inside the 'juicebox_pro.lrwebengine' folder/package). (This file should be used to replace the 'galleryInfo.lrweb' file in version 1.5.1 of the Lightroom plugin only.)

Please note that on a Mac, 'juicebox_pro.lrwebengine' is seen as a special package (rather than just a regular folder). To open the folder, you'll need to right-click the package and select 'Show Package Content'.

I hope this helps.

Juicebox will always try to load a themeUrl file and there is no way to prevent this.
If no themeUrl entry is specified in the gallery's embedding code, then Juicebox will look for (and try to load) the 'theme.css' file inside the gallery's 'jbcore/classic/' folder.
If you really want to add the contents of the 'theme.css' file to another CSS file and prevent an error 404 from occurring, then you could load a blank/empty 'theme.css' file.

There is only one version of the Juicebox-Pro v1.5.1 zip file (named 'juicebox_pro_1.5.1.zip').
When extracted, you should have a folder named 'juicebox_pro_1.5.1'.
Directly inside this folder you should see the following contents:

• adobe-lightroom-plugin (folder)

• web (folder)

• JuiceboxBuilder-Pro.air (file)

• readme.html (file)

Inside the 'adobe-lightroom-plugin' folder is the 'juicebox_pro.lrwebengine' folder/package that you would drag and drop onto your Lightroom desktop shortcut to install the 'Juicebox Plugin for Lightroom' in Windows.

As I mentioned, there is only one version of the Juicebox-Pro v1.5.1 zip file so your own zip file should contain the contents above.
If not, then perhaps your download is somehow corrupt or incomplete.
Please check the integrity of your 'juicebox_pro_1.5.1.zip' file. It should have the following properties:

Name: juicebox_pro_1.5.1.zip
Filesize: 1,912,372 bytes
MD5: 684b9d42be40906ac775aecfbb8631d8
SHA1: 872bcd0b62ef9841eab672e6a12f431919a4d969

You can check the MD5 and SHA1 hashes of files with a free program such as HashCalc.

If your own 'juicebox_pro_1.5.1.zip' file does not have the properties above, then please try re-downloading the Juicebox-Pro v1.5.1 zip file with the link from your purchase email.

I hope this helps.
Please let me know how you get on and if I can be of any further assistance.
Thank you.

You're welcome! I'm glad I could help.
I wish you well with Juicebox-Pro and your future web projects!

I'm glad to hear that you've got things sorted out.
Thank you very much for letting me know.

Here are more detailed instructions on how to upgrade Showkase to use Juicebox-Pro.

(1) Extract the Juicebox-Pro zip file ('juicebox_pro_1.5.1.zip').
The folder you will need to use is the 'jbcore' folder in this location: 'juicebox_pro_151/web/jbcore'.
If you have created a Juicebox-Pro gallery on your computer with either JuiceboxBuilder-Pro or the Juicebox-Pro Plugin for Lightroom, then you can use the 'jbcore' folder inside your gallery folder (it will be identical to the 'jbcore' folder inside the sample 'web' gallery folder).

(2) Upload the entire 'jbcore' from Step #1 above (not just its contents) to your Showkase site's 'showkase/admin/plugins/juicebox/master/' directory, overwriting the existing 'jbcore' folder in that location. (Either delete the existing 'jbcore' folder first ('showkase/admin/plugins/juicebox/master/jbcore') or ensure that your FTP program is set to overwrite existing files.)

(3) Republish your site (by clicking the 'Publish' button) to upgrade all Juicebox gallery pages throughout your Showkase site to the version of Juicebox that you have used in the procedure above.

Just to clarify, the only folder you need to upload from the Juicebox-Pro zip package is the 'jbcore' folder from the sample 'web' gallery. There is no need to upload any other files (such as the 'JuiceboxBuilder-Pro.air' file or the 'adobe-lightroom-plugin' folder).

I hope this helps.

Edit:
I've just taken a look at your website and notice that you currently use Showkase-Pro v1.7.4.
Showkase-Pro already includes Juicebox-Pro and  v1.7.4 is the latest version (please see the Version History page for details) which comes bundled with the latest version of Juicebox-Pro (v1.5.1) so your site already uses Juicebox-Pro v1.5.1 and there is no need to follow the Installing Juicebox-Pro instructions. These instructions are for Showkase-Standard users who purchase Juicebox-Pro separately (or users who have an older version of Showkase-Pro and want to upgrade Juicebox-Pro within it).
We include the Juicebox-Pro download link in your Showkase-Pro purchase so that you can use JuiceboxBuilder-Pro and the Juicebox-Pro Plugin for Lightroom (in addition to Showkase).

When using the Media Library as a source of images, a Juicebox gallery created with WP-Juicebox will display all images attached to the page or post containing the gallery shortcode.

Once the shortcode (e.g. [juicebox gallery_id="5"]) has been added to the page or post, click the 'Add Media' button (to the left of the 'Add Juicebox Gallery' button above the editor toolbar as seen in Screenshot #1 attached).
Now, just drag and drop your images into the media window which pops up.
Wait for the images to finish uploading and then close the media window via the cross at the top right (do not click the 'Insert into post' button at the bottom right).
That's all you need to do. The gallery is built dynamically at the time it is displayed so there is no need to do anything after uploading the images (other than publish your page or post).

If you want to see the images that are attached to the page or post, then in the media window, select 'Add Media (side menu) -> Media Library (tab) -> Uploaded to this post (drop-down menu)' (as seen in Screenshot #2 attached) and you'll see thumbnails of each image (which you can drag and drop into a custom order if you like). (After re-ordering images, again, just close the media window via the cross at the top right.

I hope this helps.
However, if you continue to experience difficulties, please post the URL to you gallery's web page so that I can see the gallery for myself and hopefully help further.
Thank you.

I've just checked the watermarking functionality in JuiceboxBuilder-Pro v1.5.1 using a sample PNG image with a transparent background and it seems to work OK for me (the transparency is carried through to the gallery images).
Please double-check that your own PNG image's background is actually transparent (just in case there's a problem there).
If you continue to experience difficulties, please attach the image to a post here in the forum or upload it somewhere and provide a download link so that I can investigate further and try to replicate your problem with your own image.
Thank you.

There are essentially two ways to make a Juicebox gallery responsive (with its dimensions dynamically changing with the size of the user's browser window).

Scenario #1:
A Juicebox gallery will be responsive (and will dynamically scale with the size of the user's browser window) if the gallery's own dimensions and the dimensions of all parent containers are expressed as percentages. If there is a fixed value anywhere up the chain, then the gallery's size will become fixed (e.g. 100% x 100% x 800px = 800px).
Please note that when using percentage heights, you may need to implement the suggestion noted here.

Scenario #2:
You could use JavaScript to listen for a change in the size of the user's browser window and assign new dimensions to the Juicebox gallery if and when this happens.
An example of this can be found in the resizable galleries support section here.
Take a look at the source of this sample gallery in your browser to see how this might be achieved.

Both scenarios above apply equally to Juicebox-Lite and Juicebox-Pro.

With this in mind, it can be difficult to ensure that a Drupal web page conforms to Scenario #1 and also difficult to implement Scenario #2 within a Drupal environment.

The code you provided includes the following line:

<div class="juicebox-parent " style="width: 540px; height: 450px;">

It looks like your gallery's parent container has fixed pixel dimensions and, therefore, your gallery will ultimately have a fixed size, too (even if it has dimensions expressed as percentages).

I'm not sure where the dimensions for your 'juicebox-parent' container are coming from (the module or your Drupal theme).
(Please note that the module is an unofficial plugin which we did not write ourselves.)
If these values are coming from you current gallery dimensions, then try setting your galleryWidth to be 100% (and set your galleryHeight to be a fixed pixel value (such as '600px') as your Drupal page will likely support vertical scrolling in which case the gallery would not benefit from being responsive in the vertical dimension).
Otherwise, you might like to try a different Drupal theme which does not use containers of fixed dimensions (which will constrain your gallery).